The nook treats all side loaded books as second class citizens. The way to work around this issue is to place all side loaded books into in the folder My Books, instead of the default, which is My Files.
With the Nook Glowlight Plus connected to my laptop Calibre has the following dialog under device settings:
This allowed me to set the path in this dialog to NOOK/My Books
When I plug the GlowLight 3 in and check the calibre device config, I see the following dialog box:
There is no place to add a path to drop files, so all my books are dropped under My Files.